GenoFIND Services for Microbiome

Turnkey solutions to power microbiome discovery

DNA Genotek offers a complete suite of solutions for every step of your microbiome research, from sample to answer. Customize Microbiome-On-Demand by choosing the products and services you need to optimize your study and achieve your goals.

Professional study design

Expert consulting to ensure meaningful results.

Online study management tools

Access our Study Coordinator Dashboard and our Participant Portal.

Customization and logistics

Customize our sample collection kits with your branding with a choice of single or multi-sample configurations. We can also ship sample collection kits directly to your donors.

Sampling

Optimized solutions for sample collection, nucleic acid stabilization and microbial profile snapshot from a variety of body sites and microbiomes.

Monitor the status of every sample in your study in real-time while tracking compliance data from your participants. Consolidate and view compliance metrics, sample status and more. The Study Coordinator Dashboard integrates with the Participant Portal and Single Order Fulfilment systems to bring together all of the most important study progress metrics.

Creation of a complete collection solution to reflect your requirements and your brand

Order fulfillment

DNA Genotek single order fulfillment services offer our customers the option of leveraging our established shipping and logistics expertise to deliver kits directly to their study participant. When combined with our professional customization services, this offers a full turn key solution, enabling you to focus on building your business without having to worry about managing supply chain logistics.

Sampling

Our optimized microbiome collection solutions enable you to scale from pilot to population to practice with high quality samples that ensure an accurate representation of the microbial community.

Wet lab services

CLIA accredited facility offers both 16S and shotgun sequencing.

Extraction

DNA extraction is performed using a number of manual and automation based standard operating procedures depending on the sample type that is being processed. We offer DNA extraction from multiple sample types.

16S sequencing

High-resolution taxonomic classification based on the V3-V4 16S region. This targeted sequencing method aims to amplify the 16S region of the bacterial genome which allows for species identification. Coupled with our rigorous automated DNA extraction method for recovering DNA from difficult to lyse microorganisms, we provide exceptional metagenomic sequencing.

Shotgun sequencing

This broad reaching sequencing method allows for the resulting data to be delivered in its raw form or passed onto our experienced bioinformaticians for analysis.

Bioinformatics

Our experienced bioinformaticians are able to work with raw data that is generated through our wet lab services or that has been generated at another facility. We use a robust, version controlled pipeline and curated taxonomic database to ensure consistent analysis.

Analysis

Our analytical pipelines combine bioinformatics tools and software engineering best practices like containerization and cloud computing. This lets us deliver fast turnaround-times and larger studies more economically, while maintaining complete version-control of all aspects of the analysis.

Reporting

The clean and insightful standard report provides a starting point for any microbiome analysis. The report summarizes the taxonomic data in your microbial samples and uses rigorous statistical testing to identify significant trends in your data. Designed as an easy-to-interpret introduction to the microbiome, the summary report provides a complete overview of your study results while identifying interesting areas for further research.

In addition to our Summary Report, we have expert capabilities for advanced analysis of microbial data. This includes advanced technologies for annotating the metabolic profile of the microbiome, identifying individual gene abundances, and pathogen identification for food safety and surveillance. These advanced analyses are mated with sophisticated, interactive visualizations that can be customized to your requirements.

Assays & techniques

DNA and RNA Extraction

Fully validated standard operating procedures (SOPs) are used with a number of automated and manual extraction approaches to obtain the highest quality and yield of DNA regardless of sample type.

Every DNA extraction is accompanied by a number of standard quality controls to ensure accuracy of sample assessment and ultimately better success on downstream applications. Quality control measures include:

Quantitation – Fluorescent quantitation is commonly used to accurately determine the amount of double stranded DNA in a sample. We use a method involving the fluorescent dye PicoGreen to quantitate all samples that we extract.

Purity assessment - An A260/A280 ratio is commonly used to assess the purity of a DNA sample following extraction. This can be accomplished by determining the ratio of spectrophotometric absorbance of the sample at 260 nm to that of 280 nm. We perform this assessment using a NanoDrop instrument.

Integrity assessment - DNA integrity is critical for some downstream applications and to assess this agarose gel electrophoresis is performed to visualize the DNA before it can move on for further analysis. A single band with high molecular weight (>23kb) is an indicator of good sample integrity and a smear or otherwise lower molecular weight sample is an indicator of poor sample integrity.

Gel electrophoresis image demonstrating DNA samples with varying integrity. A single band showing molecular weight of 23kB or higher such as the first lane (1) show optimal integrity and suggest that the sample should be sufficient for most downstream applications. Smearing and decreasing overall molecular weight such as the samples in the remaining lanes (2-5) suggests lesser sample integrity. Samples with lesser sample integrity may not be sufficient for some downstream applications.

Other Services

Whole Genome Amplification (WGA) – Allows you to amplify the DNA in a precious sample so that it can be used for many assays in the future without the requirement of re-collection.

Aliquotting – Sample handling that allows you to have the sample distributed across multiple tubes and reduce or eliminate future freeze-thaw damage.

Storage – Sample storage can be arranged for months or years depending on requirements in a CLIA accredited, environment controlled facility.

SNP Genotyping

Single Tube SNP Genotyping

Best for projects with:

less than 1000 samples

fewer than 50 SNPs

Technology we use is TaqMan Single Tube assays. The TaqMan assay is an allele discrimination assay using PCR amplification and a pair of fluorescent dye detectors that target the SNP. One fluorescent dye is attached to the detector that is a perfect match to the first allele (e.g. an “A” nucleotide) and a different fluorescent dye is attached to the detector that is a perfect match to the second allele (e.g. a “C” nucleotide). During PCR, the polymerase will release the fluorescent probe into solution where it is detected using endpoint analysis in a real-time instrument.

Custom Arrays

Best for projects with:

more than 1000 samples

50-500 SNPs

Technology we use is TaqMan OpenArray. This system involves the custom printing of the SNPs of interest onto an array and subsequent automated processing of those arrays.

Commercial Arrays

Best for projects with:

more than 100 samples (in some cases can be utilized with smaller sample numbers)

thousands to millions of SNPs

Platforms available:

Illumina

Affymetrix

Custom Content Available

Fragment Analysis (INDEL, VNTR or CNV)

A technology used to assess insertions or deletions in the gene sequence. We use an approach including polymerase chain reaction (PCR) to amplify the region of interest followed by capillary electrophoresis to determine the length of the fragments amplified.

Fragment analysis allows for the investigation of:

VNTRs – Variable number tandem repeats

CNVs – Copy number variants

INDELs – Insertions/deletions

Telomere Length Analysis (TLA)

This service is typically performed using a quantitative real-time PCR (qRT-PCR) method for absolute telomere length that can be found in O'Callaghan, N., V. Dhillon, P. Thomas, and M. Fenech. 2008 BioTechniques 44:807-809.

Sequencing

Best used for targeted sequencing of large fragments of DNA (e.g. whole chromosome) and whole exome sequencing.

Sanger Sequencing

Best used for targeted sequencing of small to midsized DNA fragments (i.e. 100-1,000bp).

FAQs

What services does GenoFIND offer?

GenoFIND Services offers a wide variety of services including: nucleic acid extraction, genotyping, PCR- based assays, array-based assays and sequencing-based assays. In addition to extraction and downstream applications we also are able to offer a range of scientific consulting, bioinformatics and analysis services. We have access to a wide variety of platforms and qualified scientists with years of experience working with saliva samples so if you have any questions about a specific assay or analysis please contact your Sales Representative or the Services Coordinator for more information.

What should I do if I am not sure exactly what type of assay is the best choice for my project?

Contact your Sales Representative or the Services Coordinator for more information. Based on what you hope to accomplish we can usually recommend the most suitable technology for your project. If some background research is required a consulting scientist can review the literature from your field and make project recommendations.

I am not familiar with genomics. Can you help me to understand the data once my samples have been processed?

Our reports have been designed to be straightforward and easy to read. The Services Coordinator can also help you to understand the report and describe how to interpret it. If more in-depth analysis is required a consulting scientist can review your data and provide further interpretation.

How long will it take for my services to be performed?

The turnaround time for a project will vary dramatically depending on several factors including: number of samples, type of analysis and the queue at the lab. Typically most average sized projects can be completed within 4-5 weeks from the time that samples are received but if you require more rapid turnaround please let the Services Coordinator know. Remember the earlier you are in the queue the easier it will be to accommodate your timelines so always plan ahead.

Can you store my samples?

If required, short to mid-term storage of samples may be possible for your raw or extracted samples. Please contact the Services Coordinator for more information.

What will happen to my samples once the work is complete?

If you would like unused samples returned to you for storage and future analysis please ensure that you provide return shipping information including a courier account number at the time of contract signing.

Unless otherwise stated all samples that are not returned will be retained for 30 days past the date of project completion before being destroyed.

How long will my data be stored?

Unless otherwise stated, data will be retained for 1 year from the date of project completion on a secure server before being destroyed.

How long will it take for my services to be performed?

DNA Genotek’s privacy policy and practices have been created to comply with all Canadian Federal and Provincial based privacy legislation; particularly with regards to the Personal Information Protection and Electronics Documents Act (PIPEDA). DNA Genotek follows the following ten principals of personal information compliance;

Accountability

Identifying Purposes

Consent

Limiting Collection

Limiting Use, Disclosure and Retention

Accuracy

Safeguards

Openness

Individual Access

Challenging Compliance

If you have any questions about this policy or would like further information on the ten principles please contact: privacy@dnagenotek.com.

What is a SNP?

A SNP is a single nucleotide polymorphism and refers to a change in a single base at a specific location in the genome. These point changes in the genetic code may or may not result in changes in the phenotype of the donor. Referred to as a marker, it can be used to map inherited variation among individuals, often with reference to traits.

What is an rs#?

An rs# is the reference SNP ID number that is used to identify a specific location within the genome. The rs# is used to find primers and probes that specifically map to that location in the genome and will assist in determining the donors’ genotype at that position.

DNA Genotek Inc., a subsidiary of OraSure Technologies, Inc. (NASDAQ: OSUR), focuses on providing high-quality biological sample collection products and end-to-end services for human genomics, microbiome and infectious disease applications. The Company's Oragene•Dx and ORAcollect•Dx product lines are the first and only FDA 510(k) cleared saliva-based DNA collection devices for in vitro diagnostic use. DNA Genotek also offers Research Use Only products to collect and preserve large amounts of DNA or RNA from multiple sample types. DNA Genotek markets its products worldwide and has a global customer base with thousands of customers in over 100 countries.